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verified live · 27h ago
gbif-biodiversity-mcp-server
Search GBIF species taxonomy, occurrence records, datasets, and publishers.
Tools
13
GitHub stars
1
Installs / wk
282
Licence
Apache-2.0
Transport
streamable-http, stdio
Last checked
27h ago
Tools & capabilities
13 toolsRead from the running server on 27h ago.
gbif_bulk_match_species
read-only
names*strict
Resolve up to 50 scientific names to GBIF backbone taxon keys in one call — the batch counterpart to gbif_match_species for checklist, inventory, and species-list workflows that wo… Resolve up to 50 scientific names to GBIF backbone taxon keys in one call — the batch counterpart to gbif_match_species for checklist, inventory, and species-list workflows that would otherwise need one round trip per name. Each name is matched independently and results are returned in input order, one entry per name. A name with no backbone match yields matchType NONE (no taxonKey) instead of failing the batch; a per-name lookup failure yields matchType ERROR carrying that name's error message and, when the failure was classified, a machine-readable reason — the rest of the batch is unaffected, and the call as a whole still succeeds. When a queried name is a synonym, taxonKey is the accepted taxon it resolves to and matchedTaxonKey carries the synonym's own key. Common names are not supported — use gbif_search_species for vernacular searches. Below confidence 80, review the match.
gbif_count_occurrences
read-only
yearcountrytaxonKeydatasetKeystateProvinceisGeoreferenced
+3
Count occurrences matching a taxon + location filter without fetching records. Use for quick totals ("how many Aves records in Sweden?") or before deciding whether to paginate a fu… Count occurrences matching a taxon + location filter without fetching records. Use for quick totals ("how many Aves records in Sweden?") or before deciding whether to paginate a full search. Accepts taxonKey, country (uppercase ISO 3166-1 alpha-2), publishingCountry, stateProvince, isGeoreferenced, datasetKey, year, occurrenceStatus, and iucnRedListCategory. Counts sightings only by default, matching gbif_search_occurrences — GBIF also indexes absence records, and for some taxa they are the overwhelming majority. A count above 100,001 is the signal to partition rather than page: gbif_search_occurrences cannot reach past that offset, so split the query by DATASET_KEY via gbif_occurrence_facets and search each dataset separately.
gbif_get_dataset
read-only
datasetKey*contactLimit
Fetch full dataset metadata by UUID key — title, description, citation text, contacts, license, DOI, record count, numConstituents (sub-datasets), and temporal/geographic coverage.… Fetch full dataset metadata by UUID key — title, description, citation text, contacts, license, DOI, record count, numConstituents (sub-datasets), and temporal/geographic coverage. Use after gbif_search_datasets or when an occurrence record's datasetKey needs provenance detail. Contacts are capped by contactLimit (default 10); contactsTotal and contactsReturned report the full count.
gbif_get_occurrence
read-only
occurrenceKey*
Fetch a single occurrence record by its GBIF occurrence key. Returns the complete Darwin Core record — all coordinates, administrative geography (GADM levels 0–3), dates, collectio… Fetch a single occurrence record by its GBIF occurrence key. Returns the complete Darwin Core record — all coordinates, administrative geography (GADM levels 0–3), dates, collections metadata, collector identifiers, conservation status, media links, and quality issue flags. Check occurrenceStatus before reading the record as a sighting: ABSENT means a survey looked for the taxon and did not find it. Use the occurrence key from gbif_search_occurrences results.
gbif_get_species
read-only
taxonKey*
Fetch a single backbone taxon by its GBIF taxon key. Returns full classification, authorship, taxonomic status, vernacular name, descendant count, and publication reference. Use af… Fetch a single backbone taxon by its GBIF taxon key. Returns full classification, authorship, taxonomic status, vernacular name, descendant count, and publication reference. Use after gbif_match_species when you need the complete record rather than the match summary. When taxonomicStatus is SYNONYM, acceptedKey and accepted fields identify the accepted taxon. The extinct field is absent (not false) on most records — only present on explicitly flagged taxa.
gbif_get_species_children
read-only
limitoffsettaxonKey*
List direct children of a backbone taxon — genera within a family, species within a genus, subspecies within a species. Paginated. Use gbif_match_species to get the taxonKey first,… List direct children of a backbone taxon — genera within a family, species within a genus, subspecies within a species. Paginated. Use gbif_match_species to get the taxonKey first, then iterate with offset for large groups.
gbif_get_species_classification
read-only
taxonKey*
Return the parent chain for a taxon — from kingdom (or domain) down to the immediate parent of the queried taxon — as an ordered array. Each entry has its rank, canonical name, and… Return the parent chain for a taxon — from kingdom (or domain) down to the immediate parent of the queried taxon — as an ordered array. Each entry has its rank, canonical name, and taxon key. The array is returned root-first (kingdom → phylum → class → … → immediate parent of the queried taxon); the queried taxon itself is not included — call gbif_get_species for its own record. Useful for building taxonomic trees or understanding placement without navigating the backbone level-by-level.
gbif_match_species
read-only
name*rankstrictkingdom
Match a scientific name against the GBIF backbone taxonomy. Returns the best-matching taxon with full classification and a confidence score (0–100). This is the mandatory first ste… Match a scientific name against the GBIF backbone taxonomy. Returns the best-matching taxon with full classification and a confidence score (0–100). This is the mandatory first step for any GBIF workflow — it returns the backbone taxonKey required by gbif_search_occurrences, gbif_count_occurrences, and gbif_occurrence_facets. When the queried name is a synonym, taxonKey is the accepted taxon it resolves to and matchedTaxonKey carries the synonym's own key; occurrence counts differ sharply between the two, so pass taxonKey. Below confidence 80, the match should be reviewed. matchType NONE means no usable match was found — try removing the strict flag or broadening the name.
gbif_occurrence_facets
read-only
yearfacet*countrygeometrytaxonKeydatasetKey
+7
Aggregate occurrence counts across a dimension (COUNTRY, STATE_PROVINCE, YEAR, BASIS_OF_RECORD, DATASET_KEY, KINGDOM_KEY, etc.). Returns one page of facet values ranked by count de… Aggregate occurrence counts across a dimension (COUNTRY, STATE_PROVINCE, YEAR, BASIS_OF_RECORD, DATASET_KEY, KINGDOM_KEY, etc.). Returns one page of facet values ranked by count descending — the top facetLimit at facetOffset 0, a later slice of the same ranking past that. No record payloads returned. Core tool for distribution analysis and trend queries: "which countries have the most records for this species?", "how has observation volume changed since 2010?". Scope the aggregation with taxonKey, country (uppercase ISO 3166-1 alpha-2), publishingCountry, stateProvince, year, geometry, basisOfRecord, datasetKey, occurrenceStatus, or iucnRedListCategory filters. Also the way to split a result set too large for gbif_search_occurrences to page (offset+limit caps at 100,001): facet by DATASET_KEY, then search each datasetKey on its own. Aggregates sightings only by default, matching gbif_search_occurrences and gbif_count_occurrences; to measure the presence/absence split itself, pass facet OCCURRENCE_STATUS with occurrenceStatus ANY.
gbif_search_datasets
read-only
qtypelimitoffsethostingOrgpublishingOrg
+1
Search GBIF datasets by keyword, type, publishing country (uppercase ISO 3166-1 alpha-2), publishing organization, or hosting organization. The two organization filters answer diff… Search GBIF datasets by keyword, type, publishing country (uppercase ISO 3166-1 alpha-2), publishing organization, or hosting organization. The two organization filters answer different questions — publishingOrg matches the organization whose data it is, hostingOrg the organization whose installation serves it — and an organization key from gbif_search_publishers usually wants publishingOrg. Returns dataset title, description, license, record count, and DOI. Use to find the source dataset behind a set of records, or to explore what data collections are available for a taxon, country, or organization.
gbif_search_occurrences
read-only
yearlimitmonthoffsetcountrygeometry
+13
Search 3.9B+ GBIF occurrence records with Darwin Core filters. Use taxonKey from gbif_match_species for reliable results — it resolves synonyms automatically. Accepts country (uppe… Search 3.9B+ GBIF occurrence records with Darwin Core filters. Use taxonKey from gbif_match_species for reliable results — it resolves synonyms automatically. Accepts country (uppercase ISO 3166-1 alpha-2, where the record was observed), publishingCountry (the publishing organization's country — a different question), stateProvince, bounding box (decimalLatitude/decimalLongitude ranges), WKT polygon geometry, year range, month, basis of record, coordinate filter, and dataset key. Returns sightings only by default — GBIF also indexes absence records (surveys that looked and found nothing), and occurrenceStatus controls whether they are included. Pagination is capped at offset+limit=100,001 and GBIF offers no cursor or scroll, so a larger result set is covered only by partitioning it — facet it by DATASET_KEY with gbif_occurrence_facets and search each datasetKey separately. This server cannot download a result set in bulk; that needs the GBIF Download API with a GBIF.org account, or the GBIF snapshot on AWS Open Data.
gbif_search_publishers
read-only
qlimitoffsetcountry
Search organizations registered with GBIF by name fragment or country. Returns organization key, title, and country — sufficient to chain into gbif_search_datasets as publishingOrg… Search organizations registered with GBIF by name fragment or country. Returns organization key, title, and country — sufficient to chain into gbif_search_datasets as publishingOrg for the datasets an organization published, or as hostingOrg for the ones its own installation serves, or to understand who publishes data for a region. publishingOrg is the usual chain: most organizations publish through an installation someone else runs, so hostingOrg matches nothing for them.
gbif_search_species
read-only
qrankgenuslimitfamilyoffset
+3